Type:	Package
Title:	Make 'ggplot2' Versions of Vegan's Ordiplots
Version:	0.4.3
Maintainer:	John Quensen <quensenj@msu.edu>
Description:	The 'vegan' package includes several functions for adding features to ordination plots: ordiarrows(), ordiellipse(), ordihull(), ordispider() and ordisurf(). This package adds these same features to ordination plots made with 'ggplot2'. In addition, gg_ordibubble() sizes points relative to the value of an environmental variable.
License:	GPL-2 | GPL-3 [expanded from: GPL (≥ 2)]
Encoding:	UTF-8
Depends:	R (≥ 3.2.0), ggplot2 (≥ 3.0.0), vegan (≥ 2.5-2), glue
Suggests:	formatR, permute, lattice, knitr, rmarkdown
VignetteBuilder:	knitr
URL:	https://github.com/jfq3/ggordiplots
BugReports:	https://github.com/jfq3/ggordiplots/issues
RoxygenNote:	7.2.3
NeedsCompilation:	no
Packaged:	2024-01-14 15:51:25 UTC; johnq
Author:	John Quensen [aut, cre, cph], Gavin Simpson [aut], Jari Oksanen [aut]
Repository:	CRAN
Date/Publication:	2024-01-14 16:10:02 UTC

ggordiplots: Make ggplots with ordiplot-type features.

Description

The vegan and BiodiversityR packages include several functions for adding features to ordination plots: ordiarrows, ordibubbles, ordiellipse, ordihull, ordispider, ordisurf, ordicluster. This package adds these same features to ordination plots made with ggplot2.

Functions

gg_enfit Fits vectors representing environmental variables to ordination plots.

gg_ordibubble Sizes site symbols in proportion to environmental variable.

gg_ordicluster Overlays cluster diagram on ordination plot.

gg_ordiplot Ordination plot with options for ellipses, hulls, and spiders distinguishing treatment groups.

gg_ordisurf Ordination plot with surface contours for environmental variable.

Vegan envfit plot

Description

Fits environmental parameters to an ordination plot of sites and plots them as arrows.

Usage

gg_envfit(
  ord,
  env,
  groups = NA,
  scaling = 1,
  choices = c(1, 2),
  perm = 999,
  alpha = 0.05,
  angle = 20,
  len = 0.5,
  unit = "cm",
  arrow.col = "red",
  pt.size = 3,
  plot = TRUE
)

Arguments

Value

Silently returns the plot and data frames used for the plotting if the fit of any variable is significant at alpha. Otherwise returns a message that no variable is significant.

Note

In order for the arrow tips to be labeled with the names of the variables, they must be supplied as a matrix or data frame. If a single variable is supplied as a vector, the arrow tip will be labeled with "1". A way-around is to convert the vector to a data frame with the column named for the variable.

Examples

data("varespec")
data("varechem")
vare.dist <- vegdist(varespec)
vare.mds <- monoMDS(vare.dist)
gg_envfit(ord=vare.mds, env=varechem)

data("dune")
data("dune.env")
dune.dist <- vegdist(dune)
dune.mds <- monoMDS(dune.dist)
# A1 supplied as a vector
gg_envfit(dune.mds, env=dune.env$A1, groups=dune.env$Management)
# A1 supplied as a data frame
A1 <- as.data.frame(dune.env$A1)
colnames(A1) <- "A1"
gg_envfit(dune.mds, env=A1, groups=dune.env$Management)

Ordination Bubble Plot

Description

Makes a simple ordination plot of site with the symbol size scaled to an environmental variable. Result is similar to that of BiodiversityR's ordibubble function.

Usage

gg_ordibubble(
  ord,
  env.var,
  groups = NA,
  var.label = "Level",
  choices = c(1, 2),
  plot = TRUE
)

Arguments

Value

Silently returns the plot and data frames used for the plotting.

Examples

data(dune)
data(dune.env)
dune.bray <- vegdist(dune, method = "bray")
ord <- cmdscale(dune.bray, k=(nrow(dune)-1), eig=TRUE, add=TRUE)
gg_ordibubble(ord, env.var=dune.env$A1, var.label="A1")

Add Dendrogram to Ordination Plot

Description

Modeled after the ordicluster function in vegan, this function overlays an ordination object with a cluster dendogram. Functionality has been added to include treatment groups.

Usage

gg_ordicluster(
  ord,
  cluster,
  treatments = NA,
  choices = c(1, 2),
  prune = 0,
  col = 1,
  pt.size = 3,
  plot = TRUE
)

Arguments

Details

'treatments' should be a vector of class factor and length equal to the number of samples included in the ordination and cluster; integers are not coerced into factors.

Value

Invisibly returns a list of the data frames used to make the plot (df_ord, df_segments) and the plot itself (plot).

Author(s)

Jari Oksanen, John Quensen

Examples

data(dune)
data(dune.env)
dune.bray <- vegdist(dune, method="bray")
ord <- metaMDS(dune, k=3)
cl <- hclust(dune.bray, method="complete")
gg_ordicluster(ord, cluster=cl, treatments=dune.env$Management, prune=3, col=cutree(cl, 4))

Plot with Ellipses, Hulls, Spiders

Description

gg_ordiplot uses ggplot2 to make an ordination plot with group ellipses by default, and optionally hulls and/or spiders. It is patterned after vegan's functions ordiellipse, ordihull, and ordispider and accepts similar parameters.

Usage

gg_ordiplot(
  ord,
  groups,
  scaling = 1,
  choices = c(1, 2),
  kind = c("sd", "se", "ehull"),
  conf = NULL,
  show.groups = "all",
  ellipse = TRUE,
  label = FALSE,
  hull = FALSE,
  spiders = FALSE,
  pt.size = 3,
  plot = TRUE
)

Arguments

Value

Silently returns the plot and data frames used for the plotting.

Examples

data("dune")
data("dune.env")
dune.hel <- decostand(dune, method = "hellinger")
ord <- rda(dune.hel)
gg_ordiplot(ord, groups = dune.env$Management)

Ordisurf with ggplot2

Description

Fits a surface (contour) plot of an environmental variable to an ordination plot.

Usage

gg_ordisurf(
  ord,
  env.var,
  groups = NA,
  choices = c(1, 2),
  var.label = "Level",
  binwidth,
  pt.size = 3,
  family = "gaussian",
  plot = TRUE
)

Arguments

Details

By default, 'binwidth' is calculated as the difference between minimum and maximum values of the variable divided by 15.

The colors for the points are mapped to fill; if you want to rename the legend for the groups (points), use labs(fill="New name").

See the help for stats::family for possible values for family.

Value

Silently returns the plot and data frames used for the plotting.

Note

Code for extracting plot data from the ordisurf result was taken from a blog by Oliviea Rata Burge.

Author(s)

Olivia Rata Burge, John Quensen

References

https://oliviarata.wordpress.com/2014/07/17/ordinations-in-ggplot2-v2-ordisurf/'

Examples

data(varespec)
data(varechem)
vare.dist <- vegdist(varespec)
vare.mds <- monoMDS(vare.dist)
gg_ordisurf(vare.mds, env.var = varechem$Baresoil, var.label="Bare Soil")

Make Ordination Axis Labels

Description

Makes ordination axis labels that include, if appropriate, the % total variance explained by each axis.

Usage

ord_labels(ord)

Arguments

Details

If there are no eigenvalues in ord, or if any eigenvalues are less than 0, each element of the vector returned has the form "DIMn" where n is the axis number. Otherwise, each element of the vector returned has the form "AxisN xx.x%" where "Axis" is taken from the vector of eigenvalues in ord if they are named or simply "DIM" if they are not, N is the number of the axis, and xx.x is the % of total variance explained by the axis.

Value

A character vector, each element of which can be used to label the corresponding axis of an ordination plot.

Examples

data("dune")
data("dune.env")
dune_hel <- decostand(dune, method = "hellinger")
ord <- rda(dune_hel)
axis_labels <- ord_labels(ord)
axis_labels[c(1,2)]

Scale Arrows to Plot

Description

Scales envfit arrows to fit within 75

Usage

scale_arrow(arrows, data, at = c(0, 0), fill = 0.75)

Arguments

Value

Silently returns a data frame of scaled coordinates for adding arrows to ordination plot.

Author(s)

Jari Oksanen with modifications by Gavin Simpson and John Quensen

Examples

data("varespec")
data("varechem")
vare_dist <- vegdist(varespec)
vare_mds <- monoMDS(vare_dist)
plt1 <- gg_envfit(ord=vare_mds, env=varechem, plot = FALSE)
mult <- scale_arrow(plt1$df_arrows, plt1$df_ord[ , c("x", "y")])
mult